Integrating images from multiple microscopy screens reveals diverse patterns of protein subcellular localization change

Abstract

Evaluating protein localization changes on a systematic level is a powerful tool for understanding how cells respond to environmental, chemical, or genetic perturbations. To date, work in understanding these proteomic responses through high-throughput imaging has catalogued localization changes independently for each perturbation. To distinguish changes that are targeted responses to the specific perturbation and more generalized programs, we developed a scalable approach to visualize the localization behavior of proteins across multiple experiments as a quantitative pattern. By applying this approach to 24 experimental screens consisting of nearly 400,000 images, we differentiate specific responses from more generalized ones, discover nuance in the localization behavior of stress-responsive proteins, and form hypotheses by clustering proteins with similar patterns. While previous approaches aim to capture all localization changes for a single screen as accurately as possible, our work aims to integrate large amounts of imaging data to find unexpected new cell biology.

Article and author information

Author details

  1. Alex X Lu

    Department of Computer Science, University of Toronto, Toronto, Canada
    Competing interests
    The authors declare that no competing interests exist.
  2. Yolanda T Chong

    Terrence Donnelly Centre for Cellular and Biomolecular Research, University of Toronto, Toronto, Canada
    Competing interests
    The authors declare that no competing interests exist.
  3. Ian Shen Hsu

    Department of Cell and Systems Biology, University of Toronto, Toronto, Canada
    Competing interests
    The authors declare that no competing interests exist.
  4. Bob Strome

    Department of Cell and Systems Biology, University of Toronto, Toronto, Canada
    Competing interests
    The authors declare that no competing interests exist.
  5. Louis-Francois Handfield

    Department of Computer Science, University of Toronto, Toronto, Canada
    Competing interests
    The authors declare that no competing interests exist.
  6. Oren Kraus

    Department of Electrical and Computer Engineering, University of Toronto, Toronto, Canada
    Competing interests
    The authors declare that no competing interests exist.
  7. Brenda J Andrews

    Terrence Donnelly Centre for Cellular and Biomolecular Research, University of Toronto, Toronto, Canada
    Competing interests
    The authors declare that no competing interests exist.
  8. Alan M Moses

    Department of Computer Science, University of Toronto, Toronto, Canada
    For correspondence
    alan.moses@utoronto.ca
    Competing interests
    The authors declare that no competing interests exist.
    ORCID icon "This ORCID iD identifies the author of this article:" 0000-0003-3118-3121

Funding

National Science and Engineering Research Council (Pre-Doctoral Award)

  • Alex X Lu

Canada Research Chairs (Tier II Chair)

  • Alan M Moses

Canada Foundation for Innovation

  • Brenda J Andrews
  • Alan M Moses

Canadian Institutes of Health Research (FDN-143265)

  • Brenda J Andrews

Canadian Institute for Advanced Research (Senior Fellow)

  • Brenda J Andrews

Canadian Institutes of Health Research (MOP-97939)

  • Brenda J Andrews

The funders had no role in study design, data collection and interpretation, or the decision to submit the work for publication.

Reviewing Editor

  1. Emmanuel Levy, Weizmann Institute of Science, Israel

Version history

  1. Received: September 10, 2017
  2. Accepted: March 30, 2018
  3. Accepted Manuscript published: April 5, 2018 (version 1)
  4. Version of Record published: May 4, 2018 (version 2)
  5. Version of Record updated: October 11, 2018 (version 3)

Copyright

© 2018, Lu et al.

This article is distributed under the terms of the Creative Commons Attribution License permitting unrestricted use and redistribution provided that the original author and source are credited.

Metrics

  • 2,918
    views
  • 392
    downloads
  • 24
    citations

Views, downloads and citations are aggregated across all versions of this paper published by eLife.

Download links

A two-part list of links to download the article, or parts of the article, in various formats.

Downloads (link to download the article as PDF)

Open citations (links to open the citations from this article in various online reference manager services)

Cite this article (links to download the citations from this article in formats compatible with various reference manager tools)

  1. Alex X Lu
  2. Yolanda T Chong
  3. Ian Shen Hsu
  4. Bob Strome
  5. Louis-Francois Handfield
  6. Oren Kraus
  7. Brenda J Andrews
  8. Alan M Moses
(2018)
Integrating images from multiple microscopy screens reveals diverse patterns of protein subcellular localization change
eLife 7:e31872.
https://doi.org/10.7554/eLife.31872

Share this article

https://doi.org/10.7554/eLife.31872

Further reading

    1. Cancer Biology
    2. Cell Biology
    Camille Dantzer, Justine Vaché ... Violaine Moreau
    Research Article

    Immune checkpoint inhibitors have produced encouraging results in cancer patients. However, the majority of ß-catenin-mutated tumors have been described as lacking immune infiltrates and resistant to immunotherapy. The mechanisms by which oncogenic ß-catenin affects immune surveillance remain unclear. Herein, we highlighted the involvement of ß-catenin in the regulation of the exosomal pathway and, by extension, in immune/cancer cell communication in hepatocellular carcinoma (HCC). We showed that mutated ß-catenin represses expression of SDC4 and RAB27A, two main actors in exosome biogenesis, in both liver cancer cell lines and HCC patient samples. Using nanoparticle tracking analysis and live-cell imaging, we further demonstrated that activated ß-catenin represses exosome release. Then, we demonstrated in 3D spheroid models that activation of β-catenin promotes a decrease in immune cell infiltration through a defect in exosome secretion. Taken together, our results provide the first evidence that oncogenic ß-catenin plays a key role in exosome biogenesis. Our study gives new insight into the impact of ß-catenin mutations on tumor microenvironment remodeling, which could lead to the development of new strategies to enhance immunotherapeutic response.

    1. Cell Biology
    Zhongyun Xie, Yongping Chai ... Wei Li
    Research Article

    Asymmetric cell divisions (ACDs) generate two daughter cells with identical genetic information but distinct cell fates through epigenetic mechanisms. However, the process of partitioning different epigenetic information into daughter cells remains unclear. Here, we demonstrate that the nucleosome remodeling and deacetylase (NuRD) complex is asymmetrically segregated into the surviving daughter cell rather than the apoptotic one during ACDs in Caenorhabditis elegans. The absence of NuRD triggers apoptosis via the EGL-1-CED-9-CED-4-CED-3 pathway, while an ectopic gain of NuRD enables apoptotic daughter cells to survive. We identify the vacuolar H+–adenosine triphosphatase (V-ATPase) complex as a crucial regulator of NuRD’s asymmetric segregation. V-ATPase interacts with NuRD and is asymmetrically segregated into the surviving daughter cell. Inhibition of V-ATPase disrupts cytosolic pH asymmetry and NuRD asymmetry. We suggest that asymmetric segregation of V-ATPase may cause distinct acidification levels in the two daughter cells, enabling asymmetric epigenetic inheritance that specifies their respective life-versus-death fates.